Freesurfer September 2023

freesurfer@nmr.mgh.harvard.edu

71 participants
88 discussions

Re: [Freesurfer] ScLimbic issue
by fsbuild 12 Sep '23

12 Sep '23

External Email - Use Caution  If you are getting an “illegal instruction” error running Freesurfer on Linux,  then the hardware (CPU’s) do not have those instructions available in their instruction set to execute.   As far as I know that error only happens with Freesurfer binaries compiled with AVX instructions.  So either you are running on new ARM based processors or you are running on older Intel processors (approx. pre-2011) that do not implement AVX.  There is a list of Intel processors supporting AVX instructions at https://secure-web.cisco.com/1uW45KoTvgWNrFJTk9Lu8MiuKA56yspFlAr2_S…; For Linux machines, the resolution is to run use Intel processors that can execute those instructions. - R. On Sep 12, 2023, at 16:27, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:        External Email - Use Caution        what problem? There is nothing else in your email and I don't have the previous threads.On 9/12/2023 10:51 AM, Glass, John wrote:        External Email - Use Caution        Hello, I am running into the exact same problem at my local site running version 7.4.1 on a centos 7 machine with a build stamp of: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. Has this issue been resolved? Thank you, John O. Glass, M.S.Signal Processing SupervisorDepartment of Diagnostic ImagingSt. Jude Children's Research Hospital262 Danny Thomas Place, Mail Stop 220Memphis, TN 38105-3678john.glass(a)stjude.org(901) 595-3276MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1zIIZtAoXKf8myf-KWBMwne7yPoUAd7Qy1jEcPW… Disclaimer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1Q1uNU-pDdKZt3c2gJvRAX-e_HCj8f2TfRXbDL5… Disclaimer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YLtpOgLUGV6rBo4lpwcQb-p3mwycbu6cy2hqQt… Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1banHDx6NgdG-lM1NRwrxZmZ6Z41zC38nEpucEeSW4wG4k… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] ScLimbic issue
by Glass, John 12 Sep '23

12 Sep '23

External Email - Use Caution Hello, I am running into the exact same problem at my local site running version 7.4.1 on a centos 7 machine with a build stamp of: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460. Has this issue been resolved? Thank you, John O. Glass, M.S. Signal Processing Supervisor Department of Diagnostic Imaging St. Jude Children's Research Hospital 262 Danny Thomas Place, Mail Stop 220 Memphis, TN 38105-3678 john.glass(a)stjude.org<mailto:john.glass@stjude.org> (901) 595-3276 http://secure-web.cisco.com/1cDTV5tT9Oa6ZugGCMbS5sM9mmuOcH5ETeAFbpyv_6rsfu-…<http://secure-web.cisco.com/1BpeOmGNdiCKRYBgOZ6T6GstDeTtB_1HTpS5klyKFrwc5_Q…> ________________________________ Email Disclaimer: http://secure-web.cisco.com/1uykVz0BTSeYpAi1ACN5eHA5oADlYO8HITenLBX1I7NWhN-… Consultation Disclaimer: http://secure-web.cisco.com/18gCvDjdTqEs3ScUYn27xadymDMR0ucfW9MF2xyg_dkrN2c…

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Neuroimaging data analyst position at MGH / Harvard
by Jacobs, Heidi I.,PHD 12 Sep '23

12 Sep '23

External Email - Use Caution Neuroimaging data analyst position: The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals to work as neuroimaging data analyst with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers, cognitive assessments and non-invasive vagus nerve stimulation. Do you love working with 3T MRI, 7T MRI and PET imaging, do you enjoy the challenge of integrating the acquisition and analyses of imaging data with other modalities (physiology, eye-tracking, neurostimulation,...), do you like to build new methods, imaging pipelines and integrate them with existing ones, and finally: do you have interest in the brainstem and Alzheimer' s disease? Then apply!!! This position is also open to individuals at the MSc level or at the PhD level. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. This is a lab-wide position, working in all aspects of acquiring, analyzing data from various projects, including interventions, observational studies and helping collaborators. More information: shorturl.at/mNVY6<http://secure-web.cisco.com/13GmZQEx2maK4u83hKCu53H9eVNGlKOO9A7HOihvmR4SWQJ…> [cid:image001.png@01D9E576.D629B720] Dr. Heidi Jacobs Associate Professor of Radiology Massachusetts General Hospital Harvard Medical School Department of Radiology Gordon Center for Medical Imaging 149 13th Street Charlestown, MA 02129 hjacobs(a)mgh.harvard.edu http://secure-web.cisco.com/1kLcCyBUNPIuWdfUzSthYBDZN1FF-w-Cb_JVPpxTA0xmZ4u…<http://secure-web.cisco.com/1kDMQzfTNRb5ravA9353bYWyUpVvZYUg5vdPw-lfPGyjN07…> twitter: @HeidiJacobsLab Linkedin: https://secure-web.cisco.com/12G8DNTNXVnwx9VZSaMFkLGtedcma9jdGyfKu6M6IjKYs_…

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lme and single random effect estimates
by Antonio Napolitano 12 Sep '23

12 Sep '23

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Atlas Parcellation error
by Junxia Wang 12 Sep '23

12 Sep '23

External Email - Use Caution Hello All, I used the default freesurfer command (recon-all) to generate the annotated surface file for subjects. However, the results in some subjects seem to have an obvious parcellation error. As you can see in the below graph, the area pointed by the red arrow is labelled as S_precentral-inf-part; however, we think it should be S_central. (In this particular subject, the parcellation is totally fine on the left hemisphere. The problem is only on the right hemisphere as you can see below) We adopted a solution from this answer: https://secure-web.cisco.com/1qxgC1JMOwKWxmSccucR1CmKcgaAUMcy4N4o0VjYQs9ezR… We specified three manual labels: S_central, S_temperal_sup, and S_pericallosal, to align with atlas labels and generate a new registered surface file. Adding -nonorm option made the result even better. S_central.label S_temperal_sup.label S_pericallosal.label Command #1: mris_register -L S_central.label <atlas_gcsa_file> S_central -L S_temperal_sup.label <atlas_gcsa_file> S_temperal_sup -L S_pericallosal.label <atlas_gcsa_file> S_pericallosal -curv -nonorm sub-xxxxxx/surf/rh.sphere /freesurfer/7.3.2/average/rh.average.curvature.filled.buckner40.tif rh.sphere.reg.new <atlas_gcsa_file> here is rh.destrieux.simple.2009-07-29.gcs Command #2: mris_ca_label sub-xxxxxx rh rh.sphere.reg.new <atlas_gcsa_file> rh.new.aparc.a2009s.annot The parcellation looks a lot better now but it is still not perfect (for example, look at the area pointed by the red arrow) Now, my questions are: 1. Does our solution make sense? 2. Are there any other better methods to correct the parcellation error? Thank you! Best wishes, Junxia

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Password for FS Ubuntu virtual machine
by sapere-aude＠tuta.io 11 Sep '23

11 Sep '23

External Email - Use Caution Hi, I would like the password for the user "developer" in the FreeSurfer 7.2.0 Ubuntu virtual machine. Thanks! Regards, Sapere-aude

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voxel-specific opacity
by Proulx, Jean Sebastien 11 Sep '23

11 Sep '23

External Email - Use Caution Dear Freesurfers, Is it possible to input an alpha channel to freeview? Otherwise said, can one obtain a voxel-specific opacity? I would see something like freeview underlay.mgz overlay.mgz:opacity=opacity.mgz where the single opacity value is replaced with a file containing the desired voxel-specific opacities. Thanks for your help and Have a very good day! Sebastien

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MRI analysis in Freesurfer
by Le Prieult, Yéléna 11 Sep '23

11 Sep '23

External Email - Use Caution Good afternoon, I have some questions about the analysis of the structural data in Freesurfer, it's the first I use this programm and I'm a bit lost. In order to do the recon-all command, where should I put the T1 weighted images of my subjects (3 different groups with a total of 63 subjects)? Should I put them in the subjects folder of the freesurfer folder (i.e. SUBJECTS_DIR) or should I create a new folder in this subjects folder or should I put them elsewhere? And then should I change the working directory on the terminal so the program can find my subjects? And for the recon-all command itself, once the T1 images are found, should I just write recon-all in the terminal and the preprocessing will start? Thanks a lot in advance for your answer! I really appreciate your help! Have a nice day. Best regards, Yéléna Le Prieult

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Discrepancy in vertex counts between resampled and recon-all generated annot files
by Leonardo Cardoso Saraiva 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Freesurfer Experts, I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’. In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below: mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong? Thank you for your time and attention. Best, Leo

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Watershed surfaces error
by Srishyla, Diksha 10 Sep '23

10 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to produce watershed surfaces (inner_skull, outer skull, outer skin, brain). I plan to use these for EEG functional connectivity analyses. However, they turn out faulty (image attached). Any insights as to why this might be happening? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 2) Platform: Ubuntu 22.04.3 LTS 3) recon-all.log: see attached Thank you for your time. Best, Diksha

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Freesurfer September 2023